메뉴 건너뛰기




Volumn 116, Issue 2-3, 2014, Pages 174-186

Polypharmacology rescored: Protein-ligand interaction profiles for remote binding site similarity assessment

Author keywords

Binding site similarity; Drug repositioning; Fingerprints; Polypharmacology; Profiling; Protein ligand interactions

Indexed keywords

LIGAND; MOLECULAR LIBRARY; PROTEIN; PROTEIN BINDING;

EID: 84924026602     PISSN: 00796107     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.pbiomolbio.2014.05.006     Document Type: Article
Times cited : (111)

References (87)
  • 1
    • 21044444449 scopus 로고    scopus 로고
    • Pocketome via comprehensive identification and classification of ligand binding envelopes
    • An J., Totrov M., Abagyan R. Pocketome via comprehensive identification and classification of ligand binding envelopes. Mol. Cell. Proteom. 2005, 4:752-761.
    • (2005) Mol. Cell. Proteom. , vol.4 , pp. 752-761
    • An, J.1    Totrov, M.2    Abagyan, R.3
  • 2
    • 4344668661 scopus 로고    scopus 로고
    • Drug repositioning: identifying and developing new uses for existing drugs
    • Ashburn T.T., Thor K.B. Drug repositioning: identifying and developing new uses for existing drugs. Nat. Rev. Drug. Discov. 2004, 3:673-683.
    • (2004) Nat. Rev. Drug. Discov. , vol.3 , pp. 673-683
    • Ashburn, T.T.1    Thor, K.B.2
  • 4
    • 84872859789 scopus 로고    scopus 로고
    • Molecular recognition and ligand association
    • Baron R., McCammon J.A. Molecular recognition and ligand association. Annu. Rev. Phys. Chem. 2013, 64:151-175.
    • (2013) Annu. Rev. Phys. Chem. , vol.64 , pp. 151-175
    • Baron, R.1    McCammon, J.A.2
  • 5
    • 75749103721 scopus 로고    scopus 로고
    • Atom-centered interacting fragments and similarity search applications
    • Batista J., Tan L., Bajorath J. Atom-centered interacting fragments and similarity search applications. J.Chem. Inf. Model 2010, 50:79-86.
    • (2010) J.Chem. Inf. Model , vol.50 , pp. 79-86
    • Batista, J.1    Tan, L.2    Bajorath, J.3
  • 7
    • 77953631827 scopus 로고    scopus 로고
    • Amedicinal chemist's guide to molecular interactions
    • Bissantz C., Kuhn B., Stahl M. Amedicinal chemist's guide to molecular interactions. J.Med. Chem. 2010, 53:5061-5084.
    • (2010) J.Med. Chem. , vol.53 , pp. 5061-5084
    • Bissantz, C.1    Kuhn, B.2    Stahl, M.3
  • 8
    • 77955615249 scopus 로고    scopus 로고
    • Cheminformatic analysis of biologically active macrocycles
    • Brandt W., Haupt V.J., Wessjohann L.A. Cheminformatic analysis of biologically active macrocycles. Curr. Top. Med. Chem. 2010, 10:1361-1379.
    • (2010) Curr. Top. Med. Chem. , vol.10 , pp. 1361-1379
    • Brandt, W.1    Haupt, V.J.2    Wessjohann, L.A.3
  • 9
    • 0022419375 scopus 로고
    • Aromatic-aromatic interaction: a mechanism of protein structure stabilization
    • Burley S.K., Petsko G.A. Aromatic-aromatic interaction: a mechanism of protein structure stabilization. Science 1985, 229:23-28.
    • (1985) Science , vol.229 , pp. 23-28
    • Burley, S.K.1    Petsko, G.A.2
  • 10
    • 84884376621 scopus 로고    scopus 로고
    • Leview: automatic and interactive generation of 2d diagrams for biomacromolecule/ligand interactions
    • Caboche S. Leview: automatic and interactive generation of 2d diagrams for biomacromolecule/ligand interactions. J.cheminformatics 2013, 5:40.
    • (2013) J.cheminformatics , vol.5 , pp. 40
    • Caboche, S.1
  • 11
    • 84883228319 scopus 로고    scopus 로고
    • Simg: an alignment based method for evaluating the similarity of small molecules and binding sites
    • Cai C., Gong J., Liu X., Gao D., Li H. Simg: an alignment based method for evaluating the similarity of small molecules and binding sites. J.Chem. Inf. Model 2013, 53:2103-2115.
    • (2013) J.Chem. Inf. Model , vol.53 , pp. 2103-2115
    • Cai, C.1    Gong, J.2    Liu, X.3    Gao, D.4    Li, H.5
  • 12
    • 74549149999 scopus 로고    scopus 로고
    • Predicting protein ligand binding sites by combining evolutionary sequence conservation and 3d structure
    • Capra J.A., Laskowski R.A., Thornton J.M., Singh M., Funkhouser T.A. Predicting protein ligand binding sites by combining evolutionary sequence conservation and 3d structure. PLoS Comput Biol. 2009, 5:e1000585.
    • (2009) PLoS Comput Biol. , vol.5 , pp. e1000585
    • Capra, J.A.1    Laskowski, R.A.2    Thornton, J.M.3    Singh, M.4    Funkhouser, T.A.5
  • 13
    • 34848842845 scopus 로고    scopus 로고
    • Geometry of nonbonded interactions involving planar groups in proteins
    • Chakrabarti P., Bhattacharyya R. Geometry of nonbonded interactions involving planar groups in proteins. Prog. Biophys. Mol. Biol. 2007, 95:83-137.
    • (2007) Prog. Biophys. Mol. Biol. , vol.95 , pp. 83-137
    • Chakrabarti, P.1    Bhattacharyya, R.2
  • 14
    • 84862006528 scopus 로고    scopus 로고
    • Investigation of atomic level patterns in protein-small ligand interactions
    • Chen K., Kurgan L. Investigation of atomic level patterns in protein-small ligand interactions. PLoS One 2009, 4:e4473.
    • (2009) PLoS One , vol.4 , pp. e4473
    • Chen, K.1    Kurgan, L.2
  • 15
    • 12144249613 scopus 로고    scopus 로고
    • Interaction profiles of protein kinase-inhibitor complexes and their application to virtual screening
    • Chuaqui C., Deng Z., Singh J. Interaction profiles of protein kinase-inhibitor complexes and their application to virtual screening. J.Med. Chem. 2005, 48:121-133.
    • (2005) J.Med. Chem. , vol.48 , pp. 121-133
    • Chuaqui, C.1    Deng, Z.2    Singh, J.3
  • 16
    • 84876531629 scopus 로고    scopus 로고
    • Predicting ligand binding modes from neural networks trained on protein-ligand interaction fingerprints
    • Chupakhin V., Marcou G., Baskin I., Varnek A., Rognan D. Predicting ligand binding modes from neural networks trained on protein-ligand interaction fingerprints. J.Chem. Inf. Model. 2013, 53:763-772.
    • (2013) J.Chem. Inf. Model. , vol.53 , pp. 763-772
    • Chupakhin, V.1    Marcou, G.2    Baskin, I.3    Varnek, A.4    Rognan, D.5
  • 17
    • 35248846115 scopus 로고    scopus 로고
    • 2d depiction of protein-ligand complexes
    • Clark A.M., Labute P. 2d depiction of protein-ligand complexes. J.Chem. Inf. Model 2007, 47:1933-1944.
    • (2007) J.Chem. Inf. Model , vol.47 , pp. 1933-1944
    • Clark, A.M.1    Labute, P.2
  • 18
    • 56449083729 scopus 로고    scopus 로고
    • Ligand-target interaction-based weighting of substructures for virtual screening
    • Crisman T.J., Sisay M.T., Bajorath J. Ligand-target interaction-based weighting of substructures for virtual screening. J.Chem. Inf. Model 2008, 48:1955-1964.
    • (2008) J.Chem. Inf. Model , vol.48 , pp. 1955-1964
    • Crisman, T.J.1    Sisay, M.T.2    Bajorath, J.3
  • 19
    • 0346962971 scopus 로고    scopus 로고
    • Structural interaction fingerprint (sift): a novel method for analyzing three-dimensional protein-ligand binding interactions
    • Deng Z., Chuaqui C., Singh J. Structural interaction fingerprint (sift): a novel method for analyzing three-dimensional protein-ligand binding interactions. J.Med. Chem. 2004, 47:337-344.
    • (2004) J.Med. Chem. , vol.47 , pp. 337-344
    • Deng, Z.1    Chuaqui, C.2    Singh, J.3
  • 20
    • 31544479320 scopus 로고    scopus 로고
    • Knowledge-based design of target-focused libraries using protein-ligand interaction constraints
    • Deng Z., Chuaqui C., Singh J. Knowledge-based design of target-focused libraries using protein-ligand interaction constraints. J.Med. Chem. 2006, 49:490-500.
    • (2006) J.Med. Chem. , vol.49 , pp. 490-500
    • Deng, Z.1    Chuaqui, C.2    Singh, J.3
  • 21
    • 84875479590 scopus 로고    scopus 로고
    • Encoding protein-ligand interaction patterns in fingerprints and graphs
    • Desaphy J., Raimbaud E., Ducrot P., Rognan D. Encoding protein-ligand interaction patterns in fingerprints and graphs. J.Chem. Inf. Model. 2013, 53:623-637.
    • (2013) J.Chem. Inf. Model. , vol.53 , pp. 623-637
    • Desaphy, J.1    Raimbaud, E.2    Ducrot, P.3    Rognan, D.4
  • 22
    • 79953277006 scopus 로고    scopus 로고
    • Binana: a novel algorithm for ligand-binding characterization
    • Durrant J., McCammon J. Binana: a novel algorithm for ligand-binding characterization. J.Mol. Graph. Model. 2011, 29:888-893.
    • (2011) J.Mol. Graph. Model. , vol.29 , pp. 888-893
    • Durrant, J.1    McCammon, J.2
  • 23
    • 0031226772 scopus 로고    scopus 로고
    • Empirical scoring functions: I. the development of a fast empirical scoring function to estimate the binding affinity of ligands in receptor complexes
    • Eldridge M.D., Murray C.W., Auton T.R., Paolini G.V., Mee R.P. Empirical scoring functions: I. the development of a fast empirical scoring function to estimate the binding affinity of ligands in receptor complexes. J.Comput Aided Mol. Des. 1997, 11:425-445.
    • (1997) J.Comput Aided Mol. Des. , vol.11 , pp. 425-445
    • Eldridge, M.D.1    Murray, C.W.2    Auton, T.R.3    Paolini, G.V.4    Mee, R.P.5
  • 24
    • 33750124980 scopus 로고    scopus 로고
    • Extra precision glide: docking and scoring incorporating a model of hydrophobic enclosure for protein-ligand complexes
    • Friesner R., Repasky M. Extra precision glide: docking and scoring incorporating a model of hydrophobic enclosure for protein-ligand complexes. J.Med. Chem. 2006, 49:6177-6196.
    • (2006) J.Med. Chem. , vol.49 , pp. 6177-6196
    • Friesner, R.1    Repasky, M.2
  • 25
    • 84892573390 scopus 로고    scopus 로고
    • Structural analysis of protein-ligand interactions: the binding of endogenous compounds and of synthetic drugs
    • Gallina A.M., Bork P., Bordo D. Structural analysis of protein-ligand interactions: the binding of endogenous compounds and of synthetic drugs. J.Mol. Recognit. 2014, 27:65-72.
    • (2014) J.Mol. Recognit. , vol.27 , pp. 65-72
    • Gallina, A.M.1    Bork, P.2    Bordo, D.3
  • 27
    • 84887265599 scopus 로고    scopus 로고
    • Acomprehensive survey of small-molecule binding pockets in proteins
    • Gao M., Skolnick J. Acomprehensive survey of small-molecule binding pockets in proteins. PLoS Comput Biol. 2013, 9:e1003302.
    • (2013) PLoS Comput Biol. , vol.9 , pp. e1003302
    • Gao, M.1    Skolnick, J.2
  • 28
    • 33746626424 scopus 로고    scopus 로고
    • Representation of target-bound drugs by computed conformers: implications for conformational libraries
    • Günther S., Senger C., Michalsky E., Goede A., Preissner R. Representation of target-bound drugs by computed conformers: implications for conformational libraries. BMC Bioinforma. 2006, 7:293.
    • (2006) BMC Bioinforma. , vol.7 , pp. 293
    • Günther, S.1    Senger, C.2    Michalsky, E.3    Goede, A.4    Preissner, R.5
  • 29
    • 79960809682 scopus 로고    scopus 로고
    • Old friends in new guise: repositioning of known drugs with structural bioinformatics
    • Haupt V.J., Schroeder M. Old friends in new guise: repositioning of known drugs with structural bioinformatics. Brief. Bioinform 2011, 12:312-326.
    • (2011) Brief. Bioinform , vol.12 , pp. 312-326
    • Haupt, V.J.1    Schroeder, M.2
  • 30
    • 84879269767 scopus 로고    scopus 로고
    • Drug promiscuity in pdb: protein binding site similarity is key
    • Haupt V.J., Daminelli S., Schroeder M. Drug promiscuity in pdb: protein binding site similarity is key. PLoS One 2013, 8:e65894.
    • (2013) PLoS One , vol.8 , pp. e65894
    • Haupt, V.J.1    Daminelli, S.2    Schroeder, M.3
  • 31
    • 84871126379 scopus 로고    scopus 로고
    • What can we learn from the evolution of protein-ligand interactions to aid the design of new therapeutics?
    • Higueruelo A.P., Schreyer A., Bickerton G.R.J., Blundell T.L., Pitt W.R. What can we learn from the evolution of protein-ligand interactions to aid the design of new therapeutics?. PloS one 2012, 7:e51742.
    • (2012) PloS one , vol.7 , pp. e51742
    • Higueruelo, A.P.1    Schreyer, A.2    Bickerton, G.R.J.3    Blundell, T.L.4    Pitt, W.R.5
  • 32
    • 84884686673 scopus 로고    scopus 로고
    • Hydrogen bonds in proteins: role and strength
    • Hubbard R., Haider M.K. Hydrogen bonds in proteins: role and strength. eLS 2001, 1:1-6.
    • (2001) eLS , vol.1 , pp. 1-6
    • Hubbard, R.1    Haider, M.K.2
  • 33
    • 34248594754 scopus 로고    scopus 로고
    • Crystal structures of catrocollastatin/vap2b reveal a dynamic, modular architecture of adam/adamalysin/reprolysin family proteins
    • Igarashi T., Araki S., Mori H., Takeda S. Crystal structures of catrocollastatin/vap2b reveal a dynamic, modular architecture of adam/adamalysin/reprolysin family proteins. FEBS Lett. 2007, 581:2416-2422.
    • (2007) FEBS Lett. , vol.581 , pp. 2416-2422
    • Igarashi, T.1    Araki, S.2    Mori, H.3    Takeda, S.4
  • 34
    • 84871812725 scopus 로고    scopus 로고
    • On the origins of drug polypharmacology
    • Jalencas X., Mestres J. On the origins of drug polypharmacology. MedChemComm 2013, 4:80.
    • (2013) MedChemComm , vol.4 , pp. 80
    • Jalencas, X.1    Mestres, J.2
  • 35
    • 13944256616 scopus 로고    scopus 로고
    • A"solvated rotamer" approach to modeling water-mediated hydrogen bonds at protein-protein interfaces
    • Jiang L., Kuhlman B., Kortemme T., Baker D. A"solvated rotamer" approach to modeling water-mediated hydrogen bonds at protein-protein interfaces. Proteins 2005, 58:893-904.
    • (2005) Proteins , vol.58 , pp. 893-904
    • Jiang, L.1    Kuhlman, B.2    Kortemme, T.3    Baker, D.4
  • 36
    • 84969228248 scopus 로고    scopus 로고
    • Methods to characterize the structure of enzyme binding sites
    • Kahraman A., Thornton J.M. Methods to characterize the structure of enzyme binding sites. Comput. Struct. Biol. 2008, 189-221.
    • (2008) Comput. Struct. Biol. , pp. 189-221
    • Kahraman, A.1    Thornton, J.M.2
  • 38
    • 84873030937 scopus 로고    scopus 로고
    • Comprehensive classification and diversity assessment of atomic contacts in protein-small ligand interactions
    • Kasahara K., Shirota M., Kinoshita K. Comprehensive classification and diversity assessment of atomic contacts in protein-small ligand interactions. J.Chem. Inf. Model. 2013, 53:241-248.
    • (2013) J.Chem. Inf. Model. , vol.53 , pp. 241-248
    • Kasahara, K.1    Shirota, M.2    Kinoshita, K.3
  • 39
    • 54749109580 scopus 로고    scopus 로고
    • How to measure the similarity between protein ligand-binding sites?
    • Kellenberger E., Schalon C., Rognan D. How to measure the similarity between protein ligand-binding sites?. Curr. Comput-Aid Drug. 2008, 4:209-220.
    • (2008) Curr. Comput-Aid Drug. , vol.4 , pp. 209-220
    • Kellenberger, E.1    Schalon, C.2    Rognan, D.3
  • 40
    • 10044263239 scopus 로고    scopus 로고
    • Expanded interaction fingerprint method for analyzing ligand binding modes in docking and structure-based drug design
    • Kelly M.D., Mancera R.L. Expanded interaction fingerprint method for analyzing ligand binding modes in docking and structure-based drug design. J.Chem. Inf.Comput. Sci. 2004, 44:1942-1951.
    • (2004) J.Chem. Inf.Comput. Sci. , vol.44 , pp. 1942-1951
    • Kelly, M.D.1    Mancera, R.L.2
  • 41
    • 1842411345 scopus 로고    scopus 로고
    • Energetic and entropic factors determining binding affinity in protein-ligand complexes
    • Klebe G., Böhm H. Energetic and entropic factors determining binding affinity in protein-ligand complexes. J.Recept. Signal 1997, 17.
    • (1997) J.Recept. Signal , vol.17
    • Klebe, G.1    Böhm, H.2
  • 42
    • 77952849162 scopus 로고    scopus 로고
    • Probis algorithm for detection of structurally similar protein binding sites by local structural alignment
    • Konc J., Janežič D. Probis algorithm for detection of structurally similar protein binding sites by local structural alignment. Bioinformatics 2010, 26:1160-1168.
    • (2010) Bioinformatics , vol.26 , pp. 1160-1168
    • Konc, J.1    Janežič, D.2
  • 43
    • 84857557833 scopus 로고    scopus 로고
    • Probis-database: precalculated binding site similarities and local pairwise alignments of pdb structures
    • Konc J., Cesnik T., Konc J.T., Penca M., Janežič D. Probis-database: precalculated binding site similarities and local pairwise alignments of pdb structures. J.Chem. Inf. Model 2012, 52:604-612.
    • (2012) J.Chem. Inf. Model , vol.52 , pp. 604-612
    • Konc, J.1    Cesnik, T.2    Konc, J.T.3    Penca, M.4    Janežič, D.5
  • 44
    • 44449143540 scopus 로고    scopus 로고
    • Flexophore, a new versatile 3d pharmacophore descriptor that considers molecular flexibility
    • von Korff M., Freyss J., Sander T. Flexophore, a new versatile 3d pharmacophore descriptor that considers molecular flexibility. J.Chem. Inf. Model 2008, 48:797-810.
    • (2008) J.Chem. Inf. Model , vol.48 , pp. 797-810
    • von Korff, M.1    Freyss, J.2    Sander, T.3
  • 45
    • 0030466444 scopus 로고    scopus 로고
    • Just add water! the effect of water on the specificity of protein-ligand binding sites and its potential application to drug design
    • Ladbury J.E. Just add water! the effect of water on the specificity of protein-ligand binding sites and its potential application to drug design. Chem. Biol. 1996, 3:973-980.
    • (1996) Chem. Biol. , vol.3 , pp. 973-980
    • Ladbury, J.E.1
  • 46
    • 80054911951 scopus 로고    scopus 로고
    • Ligplot+: multiple ligand-protein interaction diagrams for drug discovery
    • Laskowski R.A., Swindells M.B. Ligplot+: multiple ligand-protein interaction diagrams for drug discovery. J.Chem. Inf. Model 2011, 51:2778-2786.
    • (2011) J.Chem. Inf. Model , vol.51 , pp. 2778-2786
    • Laskowski, R.A.1    Swindells, M.B.2
  • 47
    • 84855286318 scopus 로고    scopus 로고
    • Using multiple microenvironments to find similar ligand-binding sites: application to kinase inhibitor binding
    • Liu T., Altman R.B. Using multiple microenvironments to find similar ligand-binding sites: application to kinase inhibitor binding. PLoS Comput Biol. 2011, 7:e1002326.
    • (2011) PLoS Comput Biol. , vol.7 , pp. e1002326
    • Liu, T.1    Altman, R.B.2
  • 49
    • 33846933784 scopus 로고    scopus 로고
    • Optimizing fragment and scaffold docking by use of molecular interaction fingerprints
    • Marcou G., Rognan D. Optimizing fragment and scaffold docking by use of molecular interaction fingerprints. J.Chem. Inf. Model. 2007, 47:195-207.
    • (2007) J.Chem. Inf. Model. , vol.47 , pp. 195-207
    • Marcou, G.1    Rognan, D.2
  • 51
    • 33646253652 scopus 로고    scopus 로고
    • Knowledge-based interaction fingerprint scoring: a simple method for improving the effectiveness of fast scoring functions
    • Mpamhanga C.P., Chen B., McLay I.M., Willett P. Knowledge-based interaction fingerprint scoring: a simple method for improving the effectiveness of fast scoring functions. J.Chem. Inf. Model. 2006, 46:686-698.
    • (2006) J.Chem. Inf. Model. , vol.46 , pp. 686-698
    • Mpamhanga, C.P.1    Chen, B.2    McLay, I.M.3    Willett, P.4
  • 52
    • 0033545622 scopus 로고    scopus 로고
    • Ageneral and fast scoring function for protein-ligand interactions: a simplified potential approach
    • Muegge I., Martin Y.C. Ageneral and fast scoring function for protein-ligand interactions: a simplified potential approach. J.Med. Chem. 1999, 42:791-804.
    • (1999) J.Med. Chem. , vol.42 , pp. 791-804
    • Muegge, I.1    Martin, Y.C.2
  • 53
    • 0011164114 scopus 로고    scopus 로고
    • Noncovalent interactions: a challenge for experiment and theory
    • Müller-Dethlefs K., Hobza P. Noncovalent interactions: a challenge for experiment and theory. Chem. Rev. 2000, 100:143-168.
    • (2000) Chem. Rev. , vol.100 , pp. 143-168
    • Müller-Dethlefs, K.1    Hobza, P.2
  • 54
    • 0034656949 scopus 로고    scopus 로고
    • Side-chain flexibility in proteins upon ligand binding
    • Najmanovich R., Kuttner J., Sobolev V., Edelman M. Side-chain flexibility in proteins upon ligand binding. Proteins 2000, 39:261-268.
    • (2000) Proteins , vol.39 , pp. 261-268
    • Najmanovich, R.1    Kuttner, J.2    Sobolev, V.3    Edelman, M.4
  • 55
    • 66249103972 scopus 로고    scopus 로고
    • Position specific interaction dependent scoring technique for virtual screening based on weighted protein-ligand interaction fingerprint profiles
    • Nandigam R.K., Kim S., Singh J., Chuaqui C. Position specific interaction dependent scoring technique for virtual screening based on weighted protein-ligand interaction fingerprint profiles. J.Chem. Inf. Model 2009, 49:1185-1192.
    • (2009) J.Chem. Inf. Model , vol.49 , pp. 1185-1192
    • Nandigam, R.K.1    Kim, S.2    Singh, J.3    Chuaqui, C.4
  • 56
    • 33847366247 scopus 로고    scopus 로고
    • Strong and weak hydrogen bonds in the protein-ligand interface
    • Panigrahi S.K., Desiraju G.R. Strong and weak hydrogen bonds in the protein-ligand interface. Proteins 2007, 67:128-141.
    • (2007) Proteins , vol.67 , pp. 128-141
    • Panigrahi, S.K.1    Desiraju, G.R.2
  • 57
    • 66249123260 scopus 로고    scopus 로고
    • Apif: a new interaction fingerprint based on atom pairs and its application to virtual screening
    • Perez-Nueno V.I., Rabal O., Borrell J.I., Teixidó J. Apif: a new interaction fingerprint based on atom pairs and its application to virtual screening. J.Chem. Inf. Model. 2009, 49:1245-1260.
    • (2009) J.Chem. Inf. Model. , vol.49 , pp. 1245-1260
    • Perez-Nueno, V.I.1    Rabal, O.2    Borrell, J.I.3    Teixidó, J.4
  • 59
    • 84891878468 scopus 로고    scopus 로고
    • Pyplif: Python-based protein-ligand interaction fingerprinting
    • Radifar M., Yuniarti N., Istyastono E.P. Pyplif: Python-based protein-ligand interaction fingerprinting. Bioinformation 2013, 9:325-328.
    • (2013) Bioinformation , vol.9 , pp. 325-328
    • Radifar, M.1    Yuniarti, N.2    Istyastono, E.P.3
  • 60
    • 77952683248 scopus 로고    scopus 로고
    • Structure-based approaches to target fishing and ligand profiling
    • Rognan D. Structure-based approaches to target fishing and ligand profiling. Mol. Inf. 2010, 29:176-187.
    • (2010) Mol. Inf. , vol.29 , pp. 176-187
    • Rognan, D.1
  • 61
    • 52249096127 scopus 로고    scopus 로고
    • Amolecular dynamics approach to study the importance of solvent in protein interactions
    • Samsonov S., Teyra J., Pisabarro M.T. Amolecular dynamics approach to study the importance of solvent in protein interactions. Proteins: Struct. Funct. Bioinforma. 2008, 73:515-525.
    • (2008) Proteins: Struct. Funct. Bioinforma. , vol.73 , pp. 515-525
    • Samsonov, S.1    Teyra, J.2    Pisabarro, M.T.3
  • 62
    • 75749126524 scopus 로고    scopus 로고
    • Combining machine learning and pharmacophore-based interaction fingerprint for in silico screening
    • Sato T., Honma T., Yokoyama S. Combining machine learning and pharmacophore-based interaction fingerprint for in silico screening. J.Chem. Inf. Model. 2010, 50:170-185.
    • (2010) J.Chem. Inf. Model. , vol.50 , pp. 170-185
    • Sato, T.1    Honma, T.2    Yokoyama, S.3
  • 63
    • 44349119204 scopus 로고    scopus 로고
    • Asimple and fuzzy method to align and compare druggable ligand-binding sites
    • Schalon C., Surgand J.S., Kellenberger E., Rognan D. Asimple and fuzzy method to align and compare druggable ligand-binding sites. Proteins 2008, 71:1755-1778.
    • (2008) Proteins , vol.71 , pp. 1755-1778
    • Schalon, C.1    Surgand, J.S.2    Kellenberger, E.3    Rognan, D.4
  • 64
    • 58149092163 scopus 로고    scopus 로고
    • Credo: a protein-ligand interaction database for drug discovery
    • Schreyer A., Blundell T. Credo: a protein-ligand interaction database for drug discovery. Chem. Biol. Drug. Des. 2009, 73:157-167.
    • (2009) Chem. Biol. Drug. Des. , vol.73 , pp. 157-167
    • Schreyer, A.1    Blundell, T.2
  • 65
    • 48449092564 scopus 로고    scopus 로고
    • Multibind and mappis: webservers for multiple alignment of protein 3d-binding sites and their interactions
    • Shulman-Peleg A., Shatsky M., Nussinov R., Wolfson H.J. Multibind and mappis: webservers for multiple alignment of protein 3d-binding sites and their interactions. Nucleic Acids Res. 2008, 36:W260-W264.
    • (2008) Nucleic Acids Res. , vol.36 , pp. W260-W264
    • Shulman-Peleg, A.1    Shatsky, M.2    Nussinov, R.3    Wolfson, H.J.4
  • 66
    • 0037063502 scopus 로고    scopus 로고
    • Estimates of the ab initio limit for pi-pi interactions: the benzene dimer
    • Sinnokrot M.O., Valeev E.F., Sherrill C.D. Estimates of the ab initio limit for pi-pi interactions: the benzene dimer. J.Am. Chem. Soc. 2002, 124:10887-10893.
    • (2002) J.Am. Chem. Soc. , vol.124 , pp. 10887-10893
    • Sinnokrot, M.O.1    Valeev, E.F.2    Sherrill, C.D.3
  • 67
    • 84888630744 scopus 로고    scopus 로고
    • Halogen interactions in protein-ligand complexes: implications of halogen bonding for rational drug design
    • Sirimulla S., Bailey J.B., Vegesna R., Narayan M. Halogen interactions in protein-ligand complexes: implications of halogen bonding for rational drug design. J.Chem. Inf. Model 2013, 53:2781-2791.
    • (2013) J.Chem. Inf. Model , vol.53 , pp. 2781-2791
    • Sirimulla, S.1    Bailey, J.B.2    Vegesna, R.3    Narayan, M.4
  • 68
    • 84878737382 scopus 로고    scopus 로고
    • Interplay of physics and evolution in the likely origin of protein biochemical function
    • Skolnick J., Gao M. Interplay of physics and evolution in the likely origin of protein biochemical function. Proc. Natl. Acad. Sci. U. S. A. 2013, 110:9344-9349.
    • (2013) Proc. Natl. Acad. Sci. U. S. A. , vol.110 , pp. 9344-9349
    • Skolnick, J.1    Gao, M.2
  • 70
    • 0037016451 scopus 로고    scopus 로고
    • The whole palette of hydrogen bonds
    • Steiner T. The whole palette of hydrogen bonds. Angew. Chem. 2002, 41:48-76.
    • (2002) Angew. Chem. , vol.41 , pp. 48-76
    • Steiner, T.1
  • 71
    • 78650203607 scopus 로고    scopus 로고
    • Drawing the pdb: protein-ligand complexes in two dimensions
    • Stierand K., Rarey M. Drawing the pdb: protein-ligand complexes in two dimensions. ACS Med. Chem. Lett. 2010, 1:540-545.
    • (2010) ACS Med. Chem. Lett. , vol.1 , pp. 540-545
    • Stierand, K.1    Rarey, M.2
  • 73
    • 67650468167 scopus 로고    scopus 로고
    • Utilizing target-ligand interaction information in fingerprint searching for ligands of related targets
    • Tan L., Bajorath J. Utilizing target-ligand interaction information in fingerprint searching for ligands of related targets. Chem. Biol. Drug. Des. 2009, 74:25-32.
    • (2009) Chem. Biol. Drug. Des. , vol.74 , pp. 25-32
    • Tan, L.1    Bajorath, J.2
  • 74
    • 58149116803 scopus 로고    scopus 로고
    • Similarity searching using fingerprints of molecular fragments involved in protein-ligand interactions
    • Tan L., Lounkine E., Bajorath J. Similarity searching using fingerprints of molecular fragments involved in protein-ligand interactions. J.Chem. Inf. Model 2008, 48:2308-2312.
    • (2008) J.Chem. Inf. Model , vol.48 , pp. 2308-2312
    • Tan, L.1    Lounkine, E.2    Bajorath, J.3
  • 75
    • 70349737903 scopus 로고    scopus 로고
    • Three-dimensional protein-ligand interaction scaling of two-dimensional fingerprints
    • Tan L., Vogt M., Bajorath J. Three-dimensional protein-ligand interaction scaling of two-dimensional fingerprints. Chem. Biol. Drug. Des. 2009, 74:449-456.
    • (2009) Chem. Biol. Drug. Des. , vol.74 , pp. 449-456
    • Tan, L.1    Vogt, M.2    Bajorath, J.3
  • 76
    • 77955262882 scopus 로고    scopus 로고
    • Computational methodologies for compound database searching that utilize experimental protein-ligand interaction information
    • Tan L., Batista J., Bajorath J. Computational methodologies for compound database searching that utilize experimental protein-ligand interaction information. Chem. Biol. Drug. Des. 2010, 76:191-200.
    • (2010) Chem. Biol. Drug. Des. , vol.76 , pp. 191-200
    • Tan, L.1    Batista, J.2    Bajorath, J.3
  • 77
    • 34248545940 scopus 로고    scopus 로고
    • Characterization of interfacial solvent in protein complexes and contribution of wet spots to the interface description
    • Teyra J., Pisabarro M. Characterization of interfacial solvent in protein complexes and contribution of wet spots to the interface description. Proteins: Struct. Funct. Bioinforma. 2007, 1095:1087-1095.
    • (2007) Proteins: Struct. Funct. Bioinforma. , vol.1095 , pp. 1087-1095
    • Teyra, J.1    Pisabarro, M.2
  • 79
    • 44949173950 scopus 로고    scopus 로고
    • Assessment of scaffold hopping efficiency by use of molecular interaction fingerprints
    • Venhorst J., Nunez S., Terpstra J.W., Kruse C.G. Assessment of scaffold hopping efficiency by use of molecular interaction fingerprints. J.Med. Chem. 2008, 51:3222-3229.
    • (2008) J.Med. Chem. , vol.51 , pp. 3222-3229
    • Venhorst, J.1    Nunez, S.2    Terpstra, J.W.3    Kruse, C.G.4
  • 81
    • 0036897848 scopus 로고    scopus 로고
    • Aromatic interactions in model systems
    • Waters M. Aromatic interactions in model systems. Curr. Opin. Chem. Biol. 2002, 736-741.
    • (2002) Curr. Opin. Chem. Biol. , pp. 736-741
    • Waters, M.1
  • 82
    • 75749155406 scopus 로고    scopus 로고
    • Alignment-free ultra-high-throughput comparison of druggable protein-ligand binding sites
    • Weill N., Rognan D. Alignment-free ultra-high-throughput comparison of druggable protein-ligand binding sites. J.Chem. Inf. Model 2010, 50:123-135.
    • (2010) J.Chem. Inf. Model , vol.50 , pp. 123-135
    • Weill, N.1    Rognan, D.2
  • 83
    • 13844320566 scopus 로고    scopus 로고
    • Ligandscout: 3-d pharmacophores derived from protein-bound ligands and their use as virtual screening filters
    • Wolber G., Langer T. Ligandscout: 3-d pharmacophores derived from protein-bound ligands and their use as virtual screening filters. J.Chem. Inf. Model. 2005, 45:160-169.
    • (2005) J.Chem. Inf. Model. , vol.45 , pp. 160-169
    • Wolber, G.1    Langer, T.2
  • 84
    • 36949009488 scopus 로고    scopus 로고
    • In silico elucidation of the molecular mechanism defining the adverse effect of selective estrogen receptor modulators
    • Xie L., Wang J., Bourne P.E. In silico elucidation of the molecular mechanism defining the adverse effect of selective estrogen receptor modulators. PLoS Comput Biol. 2007, 3:e217.
    • (2007) PLoS Comput Biol. , vol.3 , pp. e217
    • Xie, L.1    Wang, J.2    Bourne, P.E.3
  • 85
    • 66349119013 scopus 로고    scopus 로고
    • Aunified statistical model to support local sequence order independent similarity searching for ligand-binding sites and its application to genome-based drug discovery
    • Xie L., Xie L., Bourne P.E. Aunified statistical model to support local sequence order independent similarity searching for ligand-binding sites and its application to genome-based drug discovery. Bioinformatics 2009, 25:i305-i312.
    • (2009) Bioinformatics , vol.25 , pp. i305-i312
    • Xie, L.1    Xie, L.2    Bourne, P.E.3
  • 86
    • 0031450506 scopus 로고    scopus 로고
    • Hydrogen bonds and salt bridges across protein-protein interfaces
    • Xu D., Tasi C., Nussinov R. Hydrogen bonds and salt bridges across protein-protein interfaces. Protein Eng. 1997, 10:999-1012.
    • (1997) Protein Eng. , vol.10 , pp. 999-1012
    • Xu, D.1    Tasi, C.2    Nussinov, R.3
  • 87
    • 0036591656 scopus 로고    scopus 로고
    • Cation-pi interactions in ligand recognition and catalysis
    • Zacharias N., Dougherty D.A. Cation-pi interactions in ligand recognition and catalysis. Trends Pharmacol. Sci. 2002, 23:281-287.
    • (2002) Trends Pharmacol. Sci. , vol.23 , pp. 281-287
    • Zacharias, N.1    Dougherty, D.A.2


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.